Job ID = 2236863 sra ファイルのダウンロード中... Completed: 575517K bytes transferred in 16 seconds (290824K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 17840 0 17840 0 0 25236 0 --:--:-- --:--:-- --:--:-- 34573 100 35118 0 35118 0 0 49611 0 --:--:-- --:--:-- --:--:-- 67926 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 27183911 spots for /home/okishinya/chipatlas/results/ce10/SRX059239/SRR190679.sra Written 27183911 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:10 27183911 reads; of these: 27183911 (100.00%) were unpaired; of these: 1788033 (6.58%) aligned 0 times 21740313 (79.97%) aligned exactly 1 time 3655565 (13.45%) aligned >1 times 93.42% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3779533 / 25395878 = 0.1488 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Thu, 30 Apr 2015 11:22:38: # Command line: callpeak -t SRX059239.bam -f BAM -g ce -n SRX059239.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059239.20 # format = BAM # ChIP-seq file = ['SRX059239.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Thu, 30 Apr 2015 11:22:38: # Command line: callpeak -t SRX059239.bam -f BAM -g ce -n SRX059239.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059239.05 # format = BAM # ChIP-seq file = ['SRX059239.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Thu, 30 Apr 2015 11:22:38: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:22:38: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:22:38: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:22:38: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:22:38: # Command line: callpeak -t SRX059239.bam -f BAM -g ce -n SRX059239.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059239.10 # format = BAM # ChIP-seq file = ['SRX059239.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Thu, 30 Apr 2015 11:22:38: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:22:38: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:22:44: 1000000 INFO @ Thu, 30 Apr 2015 11:22:44: 1000000 INFO @ Thu, 30 Apr 2015 11:22:44: 1000000 INFO @ Thu, 30 Apr 2015 11:22:50: 2000000 INFO @ Thu, 30 Apr 2015 11:22:50: 2000000 INFO @ Thu, 30 Apr 2015 11:22:51: 2000000 INFO @ Thu, 30 Apr 2015 11:22:56: 3000000 INFO @ Thu, 30 Apr 2015 11:22:57: 3000000 INFO @ Thu, 30 Apr 2015 11:22:59: 3000000 INFO @ Thu, 30 Apr 2015 11:23:03: 4000000 INFO @ Thu, 30 Apr 2015 11:23:03: 4000000 INFO @ Thu, 30 Apr 2015 11:23:06: 4000000 INFO @ Thu, 30 Apr 2015 11:23:09: 5000000 INFO @ Thu, 30 Apr 2015 11:23:10: 5000000 INFO @ Thu, 30 Apr 2015 11:23:14: 5000000 INFO @ Thu, 30 Apr 2015 11:23:15: 6000000 INFO @ Thu, 30 Apr 2015 11:23:16: 6000000 INFO @ Thu, 30 Apr 2015 11:23:20: 6000000 INFO @ Thu, 30 Apr 2015 11:23:21: 7000000 INFO @ Thu, 30 Apr 2015 11:23:22: 7000000 INFO @ Thu, 30 Apr 2015 11:23:25: 7000000 INFO @ Thu, 30 Apr 2015 11:23:26: 8000000 INFO @ Thu, 30 Apr 2015 11:23:28: 8000000 INFO @ Thu, 30 Apr 2015 11:23:31: 8000000 INFO @ Thu, 30 Apr 2015 11:23:32: 9000000 INFO @ Thu, 30 Apr 2015 11:23:34: 9000000 INFO @ Thu, 30 Apr 2015 11:23:36: 9000000 INFO @ Thu, 30 Apr 2015 11:23:37: 10000000 INFO @ Thu, 30 Apr 2015 11:23:39: 10000000 INFO @ Thu, 30 Apr 2015 11:23:42: 10000000 INFO @ Thu, 30 Apr 2015 11:23:42: 11000000 INFO @ Thu, 30 Apr 2015 11:23:45: 11000000 INFO @ Thu, 30 Apr 2015 11:23:47: 11000000 INFO @ Thu, 30 Apr 2015 11:23:48: 12000000 INFO @ Thu, 30 Apr 2015 11:23:51: 12000000 INFO @ Thu, 30 Apr 2015 11:23:52: 12000000 INFO @ Thu, 30 Apr 2015 11:23:53: 13000000 INFO @ Thu, 30 Apr 2015 11:23:56: 13000000 INFO @ Thu, 30 Apr 2015 11:23:58: 13000000 INFO @ Thu, 30 Apr 2015 11:23:58: 14000000 INFO @ Thu, 30 Apr 2015 11:24:02: 14000000 INFO @ Thu, 30 Apr 2015 11:24:03: 14000000 INFO @ Thu, 30 Apr 2015 11:24:04: 15000000 INFO @ Thu, 30 Apr 2015 11:24:07: 15000000 INFO @ Thu, 30 Apr 2015 11:24:08: 15000000 INFO @ Thu, 30 Apr 2015 11:24:09: 16000000 INFO @ Thu, 30 Apr 2015 11:24:13: 16000000 INFO @ Thu, 30 Apr 2015 11:24:13: 16000000 INFO @ Thu, 30 Apr 2015 11:24:14: 17000000 INFO @ Thu, 30 Apr 2015 11:24:18: 17000000 INFO @ Thu, 30 Apr 2015 11:24:18: 17000000 INFO @ Thu, 30 Apr 2015 11:24:19: 18000000 INFO @ Thu, 30 Apr 2015 11:24:24: 18000000 INFO @ Thu, 30 Apr 2015 11:24:24: 18000000 INFO @ Thu, 30 Apr 2015 11:24:25: 19000000 INFO @ Thu, 30 Apr 2015 11:24:30: 19000000 INFO @ Thu, 30 Apr 2015 11:24:30: 19000000 INFO @ Thu, 30 Apr 2015 11:24:30: 20000000 INFO @ Thu, 30 Apr 2015 11:24:36: 20000000 INFO @ Thu, 30 Apr 2015 11:24:36: 20000000 INFO @ Thu, 30 Apr 2015 11:24:36: 21000000 INFO @ Thu, 30 Apr 2015 11:24:40: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:24:40: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:24:40: #1 total tags in treatment: 21616345 INFO @ Thu, 30 Apr 2015 11:24:40: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:24:41: 21000000 INFO @ Thu, 30 Apr 2015 11:24:41: 21000000 INFO @ Thu, 30 Apr 2015 11:24:44: #1 tags after filtering in treatment: 21612165 INFO @ Thu, 30 Apr 2015 11:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:45: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:24:45: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:24:45: #1 total tags in treatment: 21616345 INFO @ Thu, 30 Apr 2015 11:24:45: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:24:45: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:24:45: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:24:45: #1 total tags in treatment: 21616345 INFO @ Thu, 30 Apr 2015 11:24:45: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:24:47: #2 number of paired peaks: 187 WARNING @ Thu, 30 Apr 2015 11:24:47: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Thu, 30 Apr 2015 11:24:47: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:49: #1 tags after filtering in treatment: 21612165 INFO @ Thu, 30 Apr 2015 11:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:49: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:49: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:49: #1 tags after filtering in treatment: 21612165 INFO @ Thu, 30 Apr 2015 11:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:49: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:49: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:52: #2 predicted fragment length is 59 bps INFO @ Thu, 30 Apr 2015 11:24:52: #2 alternative fragment length(s) may be 2,59,83,572 bps INFO @ Thu, 30 Apr 2015 11:24:52: #2.2 Generate R script for model : SRX059239.20_model.r WARNING @ Thu, 30 Apr 2015 11:24:52: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:24:52: #2 You may need to consider one of the other alternative d(s): 2,59,83,572 WARNING @ Thu, 30 Apr 2015 11:24:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:24:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:52: #2 number of paired peaks: 187 WARNING @ Thu, 30 Apr 2015 11:24:52: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Thu, 30 Apr 2015 11:24:52: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:52: #2 number of paired peaks: 187 WARNING @ Thu, 30 Apr 2015 11:24:52: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Thu, 30 Apr 2015 11:24:52: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:57: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:57: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:57: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:57: #2 predicted fragment length is 59 bps INFO @ Thu, 30 Apr 2015 11:24:57: #2 alternative fragment length(s) may be 2,59,83,572 bps INFO @ Thu, 30 Apr 2015 11:24:57: #2.2 Generate R script for model : SRX059239.10_model.r WARNING @ Thu, 30 Apr 2015 11:24:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:24:57: #2 You may need to consider one of the other alternative d(s): 2,59,83,572 WARNING @ Thu, 30 Apr 2015 11:24:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:24:57: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:57: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:57: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:57: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:57: #2 predicted fragment length is 59 bps INFO @ Thu, 30 Apr 2015 11:24:57: #2 alternative fragment length(s) may be 2,59,83,572 bps INFO @ Thu, 30 Apr 2015 11:24:57: #2.2 Generate R script for model : SRX059239.05_model.r WARNING @ Thu, 30 Apr 2015 11:24:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:24:57: #2 You may need to consider one of the other alternative d(s): 2,59,83,572 WARNING @ Thu, 30 Apr 2015 11:24:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:24:57: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:27: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:32: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:33: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:27:38: #4 Write output xls file... SRX059239.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:38: #4 Write peak in narrowPeak format file... SRX059239.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:38: #4 Write summits bed file... SRX059239.10_summits.bed INFO @ Thu, 30 Apr 2015 11:27:38: #4 Write output xls file... SRX059239.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:38: Done! INFO @ Thu, 30 Apr 2015 11:27:38: #4 Write peak in narrowPeak format file... SRX059239.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:38: #4 Write summits bed file... SRX059239.20_summits.bed INFO @ Thu, 30 Apr 2015 11:27:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4697 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:27:52: #4 Write output xls file... SRX059239.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:52: #4 Write peak in narrowPeak format file... SRX059239.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:52: #4 Write summits bed file... SRX059239.05_summits.bed INFO @ Thu, 30 Apr 2015 11:27:52: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (12619 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。